Ok so like, the connection between caroline and GLaDOS is kinda wierd at times, but here is my personal and entirely unbiased and relevant opinion.
GLaDOS and Caroline are two seperate "consciousnesses", which both inhabit the GLaDOS core. Aperture has, time and time again, showed their capability and willingness to design fully autonomous AIs, so it's not a big leap to assume they just shoved one into the GLaDOS core too, then also ran it parallel to the other operator, who was originally supposed to be Cave Johnson, but is (or was) now Caroline.
Due to this method of running it, when the full system was activated, GLaDOS immediately became the "primary" consciousness within the system, and Caroline took a back seat. It was still an active system, and still had relatively significant influence on GLaDOS's actions, but the combination of GLaDOS being an extremely well developed AI, and the main body itself seeming to cause significant effects on the AI running it, GLaDOS ended up more or less ignoring Caroline's existence and just took it as one of the many voices going on in her head (the dampening spheres certainly did not help this process)
This system was effectively how the competing intelligences functioned, up until the entire GLaDOS system was ported into the potato. At this specific point, the only two voices left were GLaDOS and Caroline, and this large change massively affected the relationship between the competing intelligences. Then with the trigger of hearing Cave's voice again, the competing Caroline system managed to take much larger control of the primary body (PotatOS), and even start repeating some phrases.
Now once the major instance of Caroline's takover happened, the primary intelligence GLaDOS then began searching through the system for the location of the Caroline intelligence and was able to find it. Once back in her original body, GLaDOS was able to find all parts of the Caroline system, and then do what she wanted with is (honestly I'm not sure she actually deleted Caroline, might've just bluffed cause yknow, she had to keep up the Evil Heartless Robot act for like, 5 more minutes before literally serenading chell with an opera number).
Anyways thats my extended rant on the relationship between Caroline and GLaDOS
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